Sequence
atgc intronic sequence ATGC exonic sequence...ttcatctgaaattctcttccagtgatttattcagaagtcgaatacattcaaattcaagttactttagtttctgattttatctggacctctgctgtaacagTTGATGGATATCAATGAAAGTCCAGTTTATGTTCTTCTCAATCCTTCTATCAACCATTCTCAGAAGGATCTACCTGTCAGTATTTTTGAAAGTG
Basic information
species | Glycine max |
transcript | GLYMA06G47850.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G47850.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G028089_T01 (Zea mays), 3'ss of exon 2
-ttcatctgaaattctcttccagtg-atttattcagaag-tcgaatacattcaaattcaagttactttagtt--tctgattttatctggacctctgctgtaacagTTGATGGATATCAATGAAAGTCCAGTTTATGTTCTTCTCAATCCTTCTATCAACCATTCTCAGAAGGATCTACCTGTCAGTATTTTTGAAAGTG
| |||||| ||| ||| | ||| | || | | | ||||| | ||| | | || ||||| || | | | |||||||||||| | || ||||| || |||||| |||| | |||||| ||||||||| || ||||||||||| ||||| | ||||| ||| ||||
agaattgagaaattgtctgccaacatagacatttgtttgatctgtgatgtatatattcatttgactctgcataaccttcttttacttgtatattatc-----cagTTGATGGATGTTAACGAAAGCCCTGTTTATCTTCTATTAAATCCTACTATCAACCTCTCCCAGAAGGATCTCCCTGTGACTATTTATGAGAGTG
upper sequence: GLYMA06G47850.1 (Glycine max), 3'ss of exon 2
lower sequence: AT5G56280.1 (Arabidopsis thaliana), 3'ss of exon 2
ttcatctgaaattctcttccagtgatttattcagaagtcgaatacattcaaattcaagttactttagtttctgattttatctggacctctgctgtaacagTTGATGGATATCAATGAAAGTCCAGTTTATGTTCTTCTCAATCCTTCTATCAACCATTCTCAGAAGGATCTACCTGTCAGTATTTTTGAAAGTG
|||| || | | | || | | || | | | | || || | | | |||| | | | || || |||||||||||||||||||||| ||| |||||||| ||| | || ||| ||||||| || | ||||||||||| || || | ||||| ||||||||
------------gtgagtccaatgctctctctagtatttttgtataattgagatttggtctctaaaagtgtggtttttgtgtctgctcttg--gtgacagTTGATGGATATCAATGAATCTCCTGTTTATGTGCTTTTAAACCCTGCTATCAATCACACACAGAAGGATCTTCCAGTGACTATTTATGAAAGTG
upper sequence: GLYMA06G47850.1 (Glycine max), 3'ss of exon 2
lower sequence: AT4G26430.1 (Arabidopsis thaliana), 3'ss of exon 2
ttcatctgaaattctcttccagtgatttattcagaagtcgaatacattcaaattcaagttactttagtttctgattttatctggacctctgctgtaacagTTGATGGATATCAATGAAAGTCCAGTTTATGTTCTTCTCAATCCTTCTATCAACCATTCTCAGAAGGATCTACCTGTCAGTATTTTTGAAAGTG
| | | | | | || || || | ||| | | |||| | | | || | ||||||| | || || || |||| ||||||| || |||||| ||| || ||||||||| | |||||| ||||||| ||| | ||||||||||| ||||| | ||| | ||||| |
---gtgagtagtgtagctttaatgtttaatata-------aatttaattgaatttaggattctcattgtactgatttgttgaggttttcatct---acagCTGATGGACATTAATGAATCTCCTGTGTATGTTCTTTTAAATCCTGCTATCAATCATGCACAGAAGGATCTTCCTGTGACTATCTACGAAAGCG
upper sequence: GLYMA06G47850.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv19s0015g01950.t01 (Vitis vinifera), 3'ss of exon 2
ttcatctgaaattctcttccagtgatttattcagaagtcgaatacattcaaattcaagttactttagtttctgattttatctgg-acctctgctgtaacagTTGATGGATATCAATGAAAGTCCAGTTTATGTTCTTCTCAATCCTTCTATCAACCATTCTCAGAAGGATCTACCTGTCAGTATTTTTGAAAGTG
| | || || || || ||||| || ||| ||| || ||| ||| || | | | || ||||||||||||||||||| |||||||| || || ||||||||||||||||| || ||||| ||| | || |||||||| ||||| | ||| | ||||||||
-gcgtgtgttcagtggttacactgccttattttgagtgtctatatggccaatgatgtactattttccaaaaccattataacaaacatcactcttgtaacagTTGATGGATATTAATGAAAGCCCTGTCTATGTTCTTCTCAATCCGTCAATCAATCATGCACAAAAGGATCTCCCTGTGACTATCTATGAAAGTG
upper sequence: GLYMA06G47850.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S34_439V6.1 (Physcomitrella patens), 3'ss of exon 2
-ttcatctgaaattctcttccagtgatttattcagaagtcgaatacattcaaattcaagttacttta--gtttctgattttatctggacctctgctgtaacagTTGATGGATATCAATGAAAGTCCAGTTTATGTTCTTCTCAATCCTTCTATCAACCATTCTCAGAAGGATCTACCTGTCAGTATTTTTGAAAGTG
|| | | | |||| |||| || | | || | || || | | ||||||| || | | | || || | ||| | ||||| || |||||||||||||||||||| || || ||||| |||||||||| | ||||| ||||| ||| |||||||||| || || |
acaaattttgagaaacttgtcagttcccatttcaagcatcatttcggtagttatcttaactagttcaaggattctgatgtttttt---cttcctctatgtcagCTCATGGACATTAATGAAAGTCCAGTTTATGTGCTCCTGAATCCAACTATCAACCACGCACAGAAAGATCTTCCTATCAGTATTTTCGAGAGCGMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|8670223|gb|BE191330.1|BE191330EST: ATTCGACTGGGAGTGATGCAGAGGAATCAGATATGCATATTCACAAAGCT TTGATGGATATCAATGAAAGTCCAGTTTATGTTCTTCTCAATCCTTCTATC
genomic: ATTCGACTGGGAGTGATGCAGAGGAATCAGATATGCATATTCACAAAGCTgtaagtttgc ... gctgtaacagTTGATGGATATCAATGAAAGTCCAGTTTATGTTCTTCTCAATCCTTCTATC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attcaaattcaagttactttagtttctgattttatctggacctctgctgtaacagTTGATGGATATCAATGAAAGTCCAGTTTATGTTCTTCTCAATCCTTCTATCAACCATTCTCAGAAGGATCTACCTGTCAGTATTTTTGAAAGTG
ttctgat putative branch site (score: 3)
cctctgct putative PPT
tgattttat TA-rich tract
Putative cis-regulatory sequences
atgc | intron | ATGC | exonic elements by Pertea et al. |
ATGC | exon | atgc | putative intronic elements |
| | ATGC | putative exonic elements identified for retained introns |
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttcatctgaaattctcttccagtgatttattcagaagtcgaatacattcaaattcaagttactttagtttctgattttatctggacctctgctgtaacagTTGATGGATATCAATGAAAGTCCAGTTTATGTTCTTCTCAATCCTTCTATCAACCATTCTCAGAAGGATCTACCTGTCAGTATTTTTGAAAGTG
- catctga
- - - - - - -ctcttcc
- - - - - - - - - - - - - - - - - - - - - -acattca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtttctg